I popped the two cowl halves apart and was left with a pretty nice flange. I trimmed this down to about 1/4″ above the lip of the cowl.
I then taped it up, mixed up some epoxy/flox and reassembled the cowl. This will provide a structural extension to the flange of the upper cowl (were there was a tiny gap between the top and bottom halves) as well as provide a perfect fit between the flange and the inside of the upper cowl.